O94953 (KDM4B_HUMAN) Reviewed, UniProtKB/Swiss-Prot
Last modified
January 25, 2012.
Version 99.
History...
Names·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order
Names·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize orderNames and origin
| Protein names | Recommended name: Lysine-specific demethylase 4B EC=1.14.11.- Alternative name(s): JmjC domain-containing histone demethylation protein 3B Jumonji domain-containing protein 2B | ||||
| Gene names |
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| Organism | Homo sapiens (Human) | ||||
| Taxonomic identifier | 9606 [NCBI] | ||||
| Taxonomic lineage | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo |
Protein attributes
| Sequence length | 1096 AA. |
| Sequence status | Complete. |
| Protein existence | Evidence at protein level |
General annotation (Comments)
| Function | Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4 'Lys-20'. Only able to demethylate trimethylated H3 'Lys-9', with a weaker activity than KDM4A, KDM4C and KDM4D. Demethylation of Lys residue generates formaldehyde and succinate. Ref.9 |
| Cofactor | Binds 1 Fe2+ ion per subunit By similarity. |
| Subcellular location | |
| Domain | The 2 Tudor domains recognize and bind methylated histones. Double Tudor domain has an interdigitated structure and the unusual fold is required for its ability to bind methylated histone tails By similarity. |
| Sequence similarities | Belongs to the JHDM3 histone demethylase family. Contains 1 JmjC domain. Contains 1 JmjN domain. Contains 2 PHD-type zinc fingers. Contains 2 Tudor domains. |
| Sequence caution | The sequence AAC33799.1 differs from that shown. Reason: Erroneous gene model prediction. The sequence BAA74899.2 differs from that shown. Reason: Erroneous initiation. |
Ontologies
Alternative products
| This entry describes 2 isoforms produced by alternative splicing. [Align] [Select] | ||||||
| Isoform 1 (identifier: O94953-1) This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry. | ||||||
| Isoform 2 (identifier: O94953-2) The sequence of this isoform differs from the canonical sequence as follows: 373-448: SHRKRSQPKK...EDGRGKLRPT → TPPCVSPHRP...LRMATQDPCR 449-1096: Missing. | ||||||
| Note: No experimental confirmation available. |
Sequence annotation (Features)
| Feature key | Position(s) | Length | Description | Graphical view | Feature identifier | ||||
Molecule processing | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Chain | 1 – 1096 | 1096 | Lysine-specific demethylase 4B | PRO_0000183175 | |||||
Regions | |||||||||
| Domain | 15 – 57 | 43 | JmjN | ||||||
| Domain | 146 – 309 | 164 | JmjC | ||||||
| Domain | 917 – 974 | 58 | Tudor 1 | ||||||
| Domain | 975 – 1031 | 57 | Tudor 2 | ||||||
| Zinc finger | 731 – 789 | 59 | PHD-type 1 | ||||||
| Zinc finger | 851 – 907 | 57 | PHD-type 2 | ||||||
| Compositional bias | 463 – 535 | 73 | Pro-rich | ||||||
Sites | |||||||||
| Metal binding | 189 | 1 | Iron; catalytic By similarity | ||||||
| Metal binding | 191 | 1 | Iron; catalytic By similarity | ||||||
| Metal binding | 235 | 1 | Zinc By similarity | ||||||
| Metal binding | 241 | 1 | Zinc By similarity | ||||||
| Metal binding | 277 | 1 | Iron; catalytic By similarity | ||||||
| Metal binding | 307 | 1 | Zinc By similarity | ||||||
| Metal binding | 309 | 1 | Zinc By similarity | ||||||
| Binding site | 133 | 1 | Alpha-ketoglutarate By similarity | ||||||
| Binding site | 199 | 1 | Alpha-ketoglutarate By similarity | ||||||
| Binding site | 207 | 1 | Alpha-ketoglutarate By similarity | ||||||
Amino acid modifications | |||||||||
| Modified residue | 305 | 1 | Phosphothreonine By similarity | ||||||
| Modified residue | 566 | 1 | Phosphoserine Ref.7 Ref.10 | ||||||
| Modified residue | 602 | 1 | N6-acetyllysine Ref.11 | ||||||
| Modified residue | 622 | 1 | Phosphoserine Ref.7 | ||||||
| Modified residue | 1065 | 1 | Phosphothreonine Ref.10 | ||||||
Natural variations | |||||||||
| Alternative sequence | 373 – 448 | 76 | SHRKR…KLRPT → TPPCVSPHRPSQPGIWCPPG GEAKASAASWLLTTRGHGDT EAGPGLGGDPLHAQSEGQAS CVSTSRLRMATQDPCR in isoform 2. | VSP_018307 | |||||
| Alternative sequence | 449 – 1096 | 648 | Missing in isoform 2. | VSP_018308 | |||||
| Natural variant | 29 | 1 | N → T. Corresponds to variant rs11667206 [ dbSNP | Ensembl ]. | VAR_026223 | |||||
| Natural variant | 710 | 1 | K → E. Ref.1 Ref.4 Ref.5 Ref.6 Corresponds to variant rs2620836 [ dbSNP | Ensembl ]. | VAR_026224 | |||||
Sequences
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References
| « Hide 'large scale' references | |
| [1] | "Prediction of the coding sequences of unidentified human genes. XII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro." Nagase T., Ishikawa K., Suyama M., Kikuno R., Hirosawa M., Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O. DNA Res. 5:355-364(1998) [PubMed: 10048485] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), VARIANT GLU-710. Tissue: Brain. |
| [2] | "Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones." Nakajima D., Okazaki N., Yamakawa H., Kikuno R., Ohara O., Nagase T. DNA Res. 9:99-106(2002) [PubMed: 12168954] [Abstract] Cited for: SEQUENCE REVISION. |
| [3] | "The DNA sequence and biology of human chromosome 19." Grimwood J., Gordon L.A., Olsen A.S., Terry A., Schmutz J., Lamerdin J.E., Hellsten U., Goodstein D., Couronne O., Tran-Gyamfi M., Aerts A., Altherr M., Ashworth L., Bajorek E., Black S., Branscomb E., Caenepeel S., Carrano A.V. Lucas S.M.Nature 428:529-535(2004) [PubMed: 15057824] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. |
| [4] | Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. Venter J.C.Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], VARIANT GLU-710. |
| [5] | "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2), VARIANT GLU-710. Tissue: Testis. |
| [6] | "The full-ORF clone resource of the German cDNA consortium." Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A., Wiemann S., Schupp I. BMC Genomics 8:399-399(2007) [PubMed: 17974005] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 487-1096, VARIANT GLU-710. Tissue: Testis. |
| [7] | "Large-scale characterization of HeLa cell nuclear phosphoproteins." Beausoleil S.A., Jedrychowski M., Schwartz D., Elias J.E., Villen J., Li J., Cohn M.A., Cantley L.C., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 101:12130-12135(2004) [PubMed: 15302935] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-566 AND SER-622, MASS SPECTROMETRY. Tissue: Cervix carcinoma. |
| [8] | "Functional characterization of JMJD2A, a histone deacetylase- and retinoblastoma-binding protein." Gray S.G., Iglesias A.H., Lizcano F., Villanueva R., Camelo S., Jingu H., Teh B.T., Koibuchi N., Chin W.W., Kokkotou E., Dangond F. J. Biol. Chem. 280:28507-28518(2005) [PubMed: 15927959] [Abstract] Cited for: SUBCELLULAR LOCATION. |
| [9] | "Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases." Whetstine J.R., Nottke A., Lan F., Huarte M., Smolikov S., Chen Z., Spooner E., Li E., Zhang G., Colaiacovo M., Shi Y. Cell 125:467-481(2006) [PubMed: 16603238] [Abstract] Cited for: FUNCTION, ENZYME ACTIVITY. |
| [10] | "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions." Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K. Sci. Signal. 2:RA46-RA46(2009) [PubMed: 19690332] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-566 AND THR-1065, MASS SPECTROMETRY. Tissue: Leukemic T-cell. |
| [11] | "Lysine acetylation targets protein complexes and co-regulates major cellular functions." Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T., Olsen J.V., Mann M. Science 325:834-840(2009) [PubMed: 19608861] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-602, MASS SPECTROMETRY. |
| + | Additional computationally mapped references. |
Cross-references
Sequence databases | |
|---|---|
| EMBL GenBank DDBJ | AB020683 mRNA. Translation: BAA74899.2. Different initiation. AC005595 Genomic DNA. Translation: AAC33799.1. Sequence problems. AC022517 Genomic DNA. Translation: AAF31271.1. CH471139 Genomic DNA. Translation: EAW69181.1. CH471139 Genomic DNA. Translation: EAW69183.1. BC063889 mRNA. Translation: AAH63889.1. BC136611 mRNA. Translation: AAI36612.1. AL133622 mRNA. Translation: CAB63748.2. |
| IPI | IPI00013205. IPI00440491. |
| PIR | T43460. |
| RefSeq | NP_055830.1. NM_015015.2. |
| UniGene | Hs.654816. |
3D structure databases | |
| ProteinModelPortal | O94953. |
| SMR | O94953. Positions 10-346, 755-790, 917-1034. |
| ModBase | Search... |
Protein-protein interaction databases | |
| DIP | DIP-47283N. |
| IntAct | O94953. 1 interaction. |
| MINT | MINT-1427202. |
| STRING | O94953. |
PTM databases | |
| PhosphoSite | O94953. |
Proteomic databases | |
| PRIDE | O94953. |
Protocols and materials databases | |
| StructuralBiologyKnowledgebase | Search... |
Genome annotation databases | |
| Ensembl | ENST00000159111; ENSP00000159111; ENSG00000127663. |
| GeneID | 23030. |
| KEGG | hsa:23030. |
| NMPDR | fig|9606.3.peg.15454. |
| UCSC | uc002mbq.2. human. |
Organism-specific databases | |
| CTD | 23030. |
| GeneCards | GC19P004921. |
| HGNC | HGNC:29136. KDM4B. |
| MIM | 609765. gene. |
| neXtProt | NX_O94953. |
| PharmGKB | PA164721452. |
| HUGE | Search... |
| GenAtlas | Search... |
Phylogenomic databases | |
| eggNOG | prNOG06475. |
| GeneTree | ENSGT00530000063342. |
| InParanoid | O94953. |
| OMA | MLYVVPR. |
| OrthoDB | EOG4N5VW5. |
| PhylomeDB | O94953. |
Gene expression databases | |
| ArrayExpress | O94953. |
| Bgee | O94953. |
| CleanEx | HS_JMJD2B. |
| Genevestigator | O94953. |
Family and domain databases | |
| InterPro | IPR013129. TF_JmjC. IPR003347. TF_JmjC_AAH. IPR003349. TF_JmjN. IPR002999. Tudor. IPR011011. Znf_FYVE_PHD. IPR001965. Znf_PHD. IPR013083. Znf_RING/FYVE/PHD. [Graphical view] |
| Gene3D | G3DSA:3.30.40.10. Znf_RING/FYVE/PHD. 1 hit. |
| KO | K06709. |
| Pfam | PF02373. JmjC. 1 hit. PF02375. JmjN. 1 hit. [Graphical view] |
| SMART | SM00558. JmjC. 1 hit. SM00545. JmjN. 1 hit. SM00249. PHD. 2 hits. SM00333. TUDOR. 2 hits. [Graphical view] |
| SUPFAM | SSF57903. FYVE_PHD_ZnF. 1 hit. |
| PROSITE | PS51184. JMJC. 1 hit. PS51183. JMJN. 1 hit. PS50304. TUDOR. False negative. PS01359. ZF_PHD_1. False negative. PS50016. ZF_PHD_2. False negative. [Graphical view] |
| ProtoNet | Search... |
Other | |
| SOURCE | Search... |
Entry information
| Entry name | KDM4B_HUMAN | ||||||||
| Accession | Primary (citable) accession number: O94953 Secondary accession number(s): B9EGN8 Q9UF40 | ||||||||
| Entry history |
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| Entry status | Reviewed (UniProtKB/Swiss-Prot) | ||||||||
| Annotation program | Chordata Protein Annotation Program | ||||||||
| Disclaimer | Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care. | ||||||||
Relevant documents
| Human chromosome 19 Human chromosome 19: entries, gene names and cross-references to MIM |
| Human entries with polymorphisms or disease mutations List of human entries with polymorphisms or disease mutations |
| Human polymorphisms and disease mutations Index of human polymorphisms and disease mutations |
| MIM cross-references Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot |
| SIMILARITY comments Index of protein domains and families |

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